User: ariel.balter

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ariel.balter100
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Posts by ariel.balter

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Comment: C: samtools view by chromosome region chr:1000-1001000 creates "unknown reference n
... Yup! That did it. I thought I had tried that... Thanks! ...
written 7 weeks ago by ariel.balter100
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Comment: C: What Is The Fastest Method To Determine The Number Of Positions In A Bam File Wi
... I don't see an equivalent to depth or bedcov in the [sambamba docs](http://lomereiter.github.io/sambamba/docs/sambamba-view.html) ...
written 7 weeks ago by ariel.balter100
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samtools view by chromosome region chr:1000-1001000 creates "unknown reference name" error
... I'm trying to create truncated versions of my bams for testing. The [samtools docs](http://www.htslib.org/doc/samtools.html) say: > REGIONS: > > Regions can be specified as: RNAME[:STARTPOS[-ENDPOS]] and all position coordinates are 1-based. > > Important note: when multipl ...
samtools written 7 weeks ago by ariel.balter100 • updated 7 weeks ago by Pierre Lindenbaum95k
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Comment: C: What is the definition of "read depth" vs "coverage"? (again...)
... NOOOOO! That is exactly what I did not want to hear :( ...
written 7 weeks ago by ariel.balter100
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What is the definition of "read depth" vs "coverage"? (again...)
... There are a number of biostars posts on how to calculate coverage and read depth, and what they mean. I'm still confused. This is how I currently understand things: ## Depth (or Read Depth) at a BP coordinate The number of "hits" on that coordinate resulting from alignment. In other words, the num ...
read depth coverage depth written 7 weeks ago by ariel.balter100
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Comment: C: Typical costs for RNA-Seq analysis
... Looking at the first link, it's not very real-world informative. The prices range over an order of magnitude from $17/hour to $170/hour, and from $100/sample to $500/sample. AllSeq appears to be one of those services like if you search for "price for insurance" you get a website that tells you it wi ...
written 7 weeks ago by ariel.balter100
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Comment: C: Typical costs for RNA-Seq analysis
... Well, I guess I can't justify it any further than to say it has to do with the professional aspects of being a bioinformatics analyst. Perhaps we would like to know whether we are being adequately paid, or want to make a proposal to start a program. This is information we would need. But I admit it ...
written 7 weeks ago by ariel.balter100
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Forum: Typical costs for RNA-Seq analysis
... This is kind of the wrong place to post this question given that we are all analysts who do the work (mostly at universities) rather than sending it out. But I would like to know what companies that do analysis that is out-sourced generally charge. Consider an experiment such as this--three biologic ...
forum rna-seq written 7 weeks ago by ariel.balter100 • updated 7 weeks ago by Michael Dondrup42k
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Comment: C: MACS2 with multiple replicates
... Yeah I think you are probably correct based on the output I got. ...
written 10 weeks ago by ariel.balter100
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Comment: C: Why use the qvalue package instead of p.adjust in R stats?
... Hello--The link under the phrase "the same thread" points to "https://stat.ethz.ch/pipermail/bioconductor/attachments/20121219/00dc27b1/attachment.pl" which is a perl file. What link did you intend? Thanks! Something to add: When I went to the [original post](https://stat.ethz.ch/pipermail/biocondu ...
written 10 weeks ago by ariel.balter100

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